The reason I don't think that it is too heavy of a coat is this: The first light pass I had showed the "fish eyes" and adding more paint never improved them. As far as contamination this is what I did:

I wet sanded a previous water problem, cleaned with soap and water, cleaned heavily with metal prep, and finally went over the surface with a tack cloth.

Could too much hardener cause this? And would fish eye killer actually solve this problem. But if fish eye kiiller would solve it, what am I doing wrong in the first place?

Too much hardner would not cause this. If you get it in the first coat and its bad enough - better off to stop and clean it off or let it dry and wetsand and clean again before painting.

Metal Prep - is that a suface wash or an etch for bare metal (don't recall the product name...)

If its a wash did you let it evaporate or dry it off with a clean dry cloth?

Many, many people make the mistake of letting the cleaner evaporate or doing too large of an area before cleaning - what you have to do is immediately wipe off the material before it dries ~ think Karate Kid "Wax On, Wax Off"

Sometimes the rags or towels you use can leech contaminants onto the surface during the cleaning process as well.

Using soap and water is ok during some phases - but here again if any soap residue dried onto the surface that could compound problems as well.

ONLY use fisheye inhibitor as a last resort - basically you're adding silicon to the paint!

Personally I have only had to use fisheye inhibitor on a very few fiberglass cars where there was an issue.

Also -sometime when you notice light fisheyes in the first coat let it tack up really well and mist coat the next basecoat sometimes you can get it to cover.

But usually its better to stop and fix it because the fisheyes or other imperfections compound with more layers and clear.